Paradoxes and Piranhas
by Whovianfiction
Summary: The Doctor made a big mistake in his past. Even Regenerated for it. Now he has to fix it and make everything right. But Is it worth the lives of his friends Sam, Dean, and Sherlock? (SuperWhoLock)
1. Chapter 1

The Doctor rubbed his forehead, as his hands drifted down lazily over his eyes. "Headaches again?" A voice behind him piped up. It was his new companion Lyra. She wasn't human like his other companions. No, Lyra was Swelastian...Well...Half human. Her mother was human, her father was Swelastian. She looked pretty human though. You know, besides the light blue hair, and purple eyes. There was only one problem. Her being Alien, there wasn't much of the stars he could show her that she didn't already know, so they were on earth most of the time.

The Doctor just nodded at her words, as they sounded kind of fuzzy in his head. "You know you should probably get that looked at. By a _real _Doctor, I mean" She pointed out, and he glared at her. She knew as well as he did, that Time Lords didn't normally get headaches.

"I'll be fine really." He promised, opening the door to her home planet. "I just need some rest."

She nodded as she was partway out the TARDIS door. "Alright, but before I go," She started. "Tell me what happened to your last companion." She asked with a serious look on her face.

The Doctor played with the end of his new jacket, and ran a hand through his new black hair. "Clara? Well...She couldn't quite handle regeneration." He said with a clinch in his tone, and just looked down. "Said she needed some time to think and take a break. When I came back, I didn't quite get the timing right...She...Became an old woman, and died of a heart attack. Died waiting for me."

Lyra felt it was a touchy subject, but needed to know a bit more. "Couldn't you just go back in time and get her?"

The Doctor shook his head. "It's a fixed time, she spent all those years without me, I can't change that."

Lyra nodded, looking down now also. "You should get your rest," She said after a long silence. "Get better Doc." She stepped out of the TARDIS, and said her goodbyes, watching the TARDIS fly away.

The Doctor sighed, thirteen lifetimes seemed too long sometimes. "Something wrong dear?" The voice came from a younger(er) woman, blonde, rather sassy, had her own gun.

The Doctor turned to his wife. "Headaches again." He said affirming her thoughts.

_Stop. I (your reader) thought River was dead?  
Yes...Well...Spoilers._

River walked up behind him rubbing his shoulders. "You know there's only one thing that could cause those, right?"

The Doctor nodded, letting another sigh escape his lips. "What do I do?" He said turning to look at her new facial features. To him, it was odd. Almost like seeing regeneration, yet not at all. River had died at the library, but he saved her to a hard drive system. All he had to do, was re-download her to to another compatible body. Which, he wasn't quite sure why it took him so long to figure out.

River looked him straight in the eye with almost a glare. "You know what you have to do."

"I can't! You know I can't!"

"You're just to much of a coward to go talk to her!"

"And what am I supposed to say? 'Hey Clara! I screwed up your life! Want to go on another adventure?"

"Sweetie, I barely think that regenerating and getting her long lost sister killed off is hardly something you should blame yourself."

"I don't blame myself! She blames me! And we all know it!"

There was a silence for a while before River piped up. "The paradox you created for her is causing the headaches. Paradoxes for Time Lords is like a sickness, it always ends up with side effects."

"River, please don't make me do this." He pleaded

"I'm not making you do anything." She pointed out. "Besides, I'm not the one getting the headaches." She sassed, and walked out of the room.

The TARDIS hummed, as the Doctor slummed down into one of the chairs in the console room, running his hand over his eyes again. The headache would go away eventually, but he would keep getting them until he fixed this. When was he going to fix this? How was he going to fix this? Clara would end up dying instead of her sister, and things would be much worse...for him. He knew he was being completely selfish about the situation, but he didn't want to lose Sam, Dean, and Sherlock too. There must be something he could do.


	2. Chapter 2

He sat in the TARDIS aone, his hands covering his face. How could he have let this happen?

_**a Previous regeneration earlier.**_

"Where would you like to go today Clara?" He asked with a cheerful smile clapping his hands together.

"Well.." She looked lost in thought, then pulled out her book of places she wanted to go, and flipped through the pages.

His heart sank. The way she flipped through reminded him of River, and the smile fell off his face.

"Doctor?" Clara asked, pulling him out of his thoughts.

"Hmm?" The Doctor asked, masking his face with a smile.

"Are you alright?"

"Perfectly fine." He said bluntly and returned to the console.

"Doctor," She started. "Look at this." She turned the TARDIS screen to show him reports.

The Doctor carefully examined the screen carefully. He smiled and laughed. "Care to meet a few friends of mine?"

Clara looked confused. "What does a murder have to do with meeting some of your friends? I thought you don't like killings?"

"_**I**_ Don't. But they do, and I can promise you they'll be there." He said with a smile, dancing around the console and straightening his bow tie.

"So we're going to America?"

"And London. We still have yet to collect the whole crew you know."

"Whole crew? I thought I was the crew." She said almost about to pout.

"Silly Clara." He said with a laugh and patted her head.

"That's reassuring." She mumbled, crossing her arms. "The last 'crew' I found out about turned out to be your dead wife." She mumbled under her breath. And of course, the Doctor didn't hear. A part of Clara was slowly falling in love with the Doctor. Maybe that's why the TARDIS hated her. But then again, the TARDIS didn't hate River from the sounds of it. But there was a secret she kept from the doctor. _She_ was the one who saved River from the library. Heck, she's probably out having adventures right now. But River asked Clara not to tell him, that she would be back one day to explain everything.

"Here we are!" He said with a nod, snapping the doors to the TARDIS to 2013 London.

"Who are we picking up?" She asked curiously.

"Sherlock Holmes." he stated bluntly.

If Clara was drinking anything, she would have spit it out. "Sherlock Holmes? He's real?"

"Of course he's real! Where do you think they get the ideas for the books from? Pay attention Clara!" He said straightening his jacket and stepping a foot out on the London streets.

Of course, it smelled like rain. It _Always_ Smelled like rain.  
The streets seemed calm today, and he could see the London eye. "Baker street" He mumbled to himself looking around. "Baker street...Baker street...Ah Ha!" He said finding the door to the flat marked '221B' and knocked on the door. "Mrs Hudson!" He yelled. "Mrs Hud-!" He was interrupted by the door opening.

"Why hello Doctor!" The frail old women greeted him with a hug.

"Is Sherlock home?" The Doctor asked.

Her face fell. "You haven't heard...Have you?"

The Doctor shook his head and became worried. Had something happened to the consulting detective?

"He's passed on."

The Doctors face fell. "I did come to 2013, correct?"

She nodded.

"Not of old age then?"

She shook her head.

"Well thank you anyways." He muttered glumly. "Tell John I said hello"

"He's in if you would like to speak to him."

A tiny little spark was on the Doctor's face now.

"He's talking with his sister Harry, but I'm sure he wouldn't mind." Mrs. Hudson said with a nod.

"I would love to!"

Mrs. Hudson lead them up to the flat where there were to figures sitting in chairs, facing away from him.  
But that voice! He knew that voice!

He walked in, and when he approached to sit in a chair across from them he realized...John's sister. Couldn't be John's sister because he knew that person by a much, much, much, different name. "River?" He mumbled in astonishment.


	3. Chapter 3

River smiled calmly, taking a sip of her tea "Hello, sweetie." Her smile was almost a smirk, and it taunted the Doctor as he straightened his bow tie.

"Harry." John interrupted, standing up to greet the Doctor with a firm handshake.

The Doctor looked confused and shook his hand, then licked it and slicked his hair back.

"She's been going by the name Harry, she's my sister." John stated.

"But- How?- Amy?"

"Couldn't have children." River finished his sentence with a nod. "If you remember correctly, you sent my parents back in time and they adopted."

The Doctor pointed at John in astonishment, "But- You? - Anthony?"

John nodded. "John _Anthony_ Watson"

"Brother-in-law?" The Doctor squeaked, pulling his now seemingly tight bow tie off of his neck.

John looked as if he was going pale. "Brother-in-law?" John questioned, sending River a look.

River smirked and winked at him, taking another sip of her tea.

"You two?" John questioned, suddenly needing to sit down again.

The Doctor's face reddened with a blush.

River laughed and stood up and gave him a peck on the cheek. " 'fraid so brother." She straightened his bow tie carefully, he had messed it up so with all his flailing, after all. He was so cute when he blushed though.

Clara coughed. She felt sort of awkward at this family reunion. "So!" She interrupted, "Would you mind telling us about Sherlock?"

As if John's face wasn't pale enough already, if he got any whiter, he would look like a sheet of paper, and the slight smile fell a million miles from his face. "Ah, yes, Sherlock..." He trailed off, looking down at the floor.

The Doctor nudged Clara, and they both took a seat, "I was getting to that." He muttered. "No need to be insensitive." But really he was just upset he didn't get to ask.

River sat back down as well, rubbing John's back lovingly. She knew how much the loss of his friend had upset him. She consoled him for the first month of Sherlock's death.

John shook his head, obviously overhearing what The Doctor had said, then looked up at River, and she nodded. "I can do this." He took Rivers other hand with a squeeze "He jumped off a building...To-To save me." His throat was getting choked as he tried to form words. "Moriarty had guns trained on me, and the only way his men would stop, is if Sherlock jumped off that building." He itched a spot on his newly grown mustache, trying to stop his stinging eyes.

The Doctor nodded sadly, not knowing what else to say. He knew what it was like to lose someone. He caught River's glance for a moment, then kneeling in front of John and taking his hands. "What if he's not dead?"

"Doctor, he's a clever man, but they buried him, I saw." John protested. He had spent months trying not to blame himself for Sherlock's death, he didn't want to add false hopes on top of that.

"John, I know what it's like to lose someone," He looked straight at River while he was talking, not even knowing if this River was from his time stream, "And you never know," He started with a faint smile. "You never know where they might pop up again." He added with a wink.

River looked back at him. How was she supposed to explain how she was back from the library? She tried not to show her emotion as the Doctor looked at her, but she could feel her eyes begin to sting.

"Doctor?" John questioned. "Do you know something I don't?" He asked with a quirked eyebrow.

"Spoilers!" The Doctor said, winking at River, and hoping up, only to spin around.


End file.
